Switching between subjective and objective modes is the essence of the scientific modus operandi. Not many people seem to appreciate that. Science is all about riding two horses, maybe not in concert, but certainly alternately - and knowing when to switch from one to the other.

I strongly recommend it, especially as there are faint echoes of the thinking in this posting of mine from way back in 2009.

Start of original posting:

An opportunity has just presented itself to share with my fellow earthlings an idea that's been fermenting in this senescent brain for some time. It concerns the building blocks of DNA and RNA - the purine and pyrimidine bases. These are the flat stackeable molecules that make up the base pairs in double-stranded DNA - Watson and Crick's double helix- and thence the triplet genetic code.

Left: pyrimidines and purines. Right: a pyrimidine nucleotide showing the intermediate ribose sugar between a pyrimidine base and phosphate

Why were these particular molecules selected from the primeval soup? Could other molecules have served in their place? Did adenine and guanine (the purines) and cytosine, thymine and uracil (the pyrimidines) just happen to be "lying around", so to speak, in some primeval rock pool, or forming in the vicinity of a hydrothermal vent?

I tried tackling it first from a physicochemical standpoint. What conditions would be needed for any kind of spontaneous chemistry to occur in a puddle say on Earth? The classic Miller-Urey experiments you may recall subjected the assumed constituents of Earth's proto-atmosphere to electric discharges, in an attempt to generate the precursors of proteins and nucleic acids (amino acids, purines and pyrimidines). Glycine - the simplest of the amino acids- was formed, but that was hardly a chemical cornucopia.

The Miller-Urey apparatus. The test mixture of water, methane, ammonia, hydrogen and carbon monoxide was intended to replicate the then-imagined reducing atmosphere. Current thinking is that the main carbon component was CO2 rather than methane CH4. Interestingly, substituting CO2 for methane gives the same range of amino acid and other products, provided that oxygen is excluded.See wiki for more details

One of the chief problems would have been intense uv radiation from space - without oxygen, there would have been no ozone "sun-screen". So maybe the first requirement was to generate sun-screen agents in situ. Purines and pyrimidines all absorb strongly in the ultraviolet:

So if they formed by accident a kind of proto-Darwinian natural selection would operate. Further molecules could then evolve, protected by the sun-screen molecules. What about the sugars - the five carbon ribose and deoxyribose? Could they have developed initially in a permissive role, simply to allow more chemistry to proceed?

If life did evolve on land, say in a rock pool receiving intermittent rain, and exposed to all weathers, then there needed to be a mechanism to protect against freezing or evaporation. Chemistry generally needs to be in solution if one is to synthesise. Well, there's a possible role for sugars. Firstly, they depress freezing point, ie have anti-freeze properties. What's more, a sugar solution tends to go syrupy when water is evaporated. It's often quite difficult to drive off the last of the water. Sugar molecules bristle with hydrogen-bonding OH groups which cling tenaciously to water.

Sun-screen agent, anti-freeze - are these the properties of purines, pyrimidines and sugars that caused them to become the building blocks of life?

What about those five chemical bases? Where did the carbon and nitrogen come from for their cyclic structures?

It was the article in the current New Scientist ("Was life founded on cyanide from space crashes?") that provided another piece of the jigsaw. It's proposed that life on earth was seeded by cyanide , -CN, in asteroids. As written it's a free radical, not a stable molecule. It would have to be HCN, or a metal cyanide, eg KCN. Now if you look at the detailed structure of purines and pyrimidines, you will see that all of them feature an alternation of -C-N- in their rings. There are some -C-C bonds as well, but the cyanide dimer cyanogen N-C-C-N could have provided that.

As soon as I started googling I struck pay dirt, with a 1978 paper describing how solutions of HCN began to form purines and pyrimidines spontaneously in the presence of alkali.

Read the New Scientist article and comments, five at the time of writing, with the suggestion that cyanide is the carbon precursor par excellence, not only for its association with nitrogen, but for being "electron-rich" (my term), given the presence of that triple bond between the two atoms, representing three shared pairs of electrons.

Standard valence formula (lower left); electronic configuration (upper right). Of the six electrons in the triple bond, 4 are available for forming new chemical bonds with additional atoms of carbon, nitrogen, hydrogen etc.

Further reading: for a critique of the Miller-Urey experiment, indeed, the entire idea that life could have evolved spontaneously, see the article by John Peet.

It's nigh on 7 years since penning this post, which still continues to receive a trickle of visitors, according to my sitemeter. Much water has flowed undr this blogger's bridge these last few years. First there's this retired science bod's explanation for the Turin Shroud- a flour/oil imprint from a live adult male (probably 13th century!) onto linen intitially, then roasted, then washed, to produce the final faint, enigmatic 'negative' image. See my specialist TS site for details.

There's also my theory forStonehenge, and indeed most standing stones, circles and henges in the UK, namely that they were sites for "sky burial", or as I prefer to call it, AFS (avian-facilitated skeletonization). See the most recent postings on this site for the basis of this interpreation, much resting on the crude and rustic layout of what has been dubbed "Seahenge" uncovered by storms on the Norfolk coast in the late 1990s.

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About Me

Colin Berry, aka sciencebod, is a retired PhD researcher/teacher/academic who has worked in industry, medical schools, schools, food and biomedical research (mainly in the UK, but also in W.Africa and the United States). He's best known for his work on RESISTANT STARCH, recently described as "the trendiest form of dietary fibre".
See also his specialist Shroud of Turin blog on www.shroudofturinwithoutallthehype.wordpress.com
with over 200 postings to date.

Create one's own blog (age, class, gender no barrier)

It's really quite straightforward. All one has to do is to click on the photograph with that nice young man. One can then be part of the frightfully interesting Blogger community in just a couple of jiffs.

Acknowledgment

What's the latest on the LHC?

LHC gets warning system upgrade : BBC 28 September 2009

Self-organization

From wiki entry on SELF ORGANIZATION: "As a result, processes considered part of thermodynamically open systems, such as biological processes that are constantly receiving, transforming and dissipating chemical energy (and even the earth itself which is constantly receiving and dissipating solar energy), can and do exhibit properties of self organization far from thermodynamic equilibrium."

How far away should your off-licence be for a bottle of wine to be energy-neutral?

What do these two have in common?

Answer: both arrived in this world about the same time. Sir Isaac Newton was born on 4th Jan 1643 (new style*). The Taj Mahal had a 20 year gestation period, centred on approximately the same year. Click on piccy for an older post .* Or Christmas Day, 1642, depending which dating system one uses.

Is interstellar space travel feasible?

The nearest star (more correctly, star system, since it's 3 stars, a binary and a smaller satellite star) is Alpha Centauri. The average distance from Earth is 4.3 light years. Suppose technology allows us one day to achieve an interstellar cruising speed of half the speed of light. A comfortable acceleration of g (simulating Earth's gravity) would take a year, with another year to slow down comfortably. The entire journey from Earth would take a minimum of 10 years approximately. Having arrived at one's destination, it would take 4.3 years to send a radio postcard (" Hello Mum and Dad. Have arrived safely, and am now looking for a habitable planet. Am hoping it's hiding behind Proxima. Have looked everywhere else... Would die for some Cheddar cheese... ")

Watch this space

It's a cheap and cheerful form of transcendental meditation.(experimenting with settings, actually)

What causes weather?

Could you answer that question in just 7 words, ie " weather is due to...? Need some help, " Weather is due to t- - u - - - - - - h - - - - - - o - t - - E- - - -'s s - - - - - - ." The National Curriculum (England and Wales) does have its uses, but there are many more such simple principles, expressed in a minimum of words, that could be usefully incorporated.

"Had there been a Beginning (there wasn't, as it happens), there would initially have been complete Nothingness. But just as Nature abhors a vacuum, it's totally gutted at the thought of Nothingness. I mean to say - how far does Nothingness extend, assuming it has one of more dimensions? It can't extend for an infinite distance, since that would be a physical impossibility. Nothingness, to avoid having infinite reach, coils up on itself to acquire finite dimensions. In so doing, it becomes Somethingness, which has a spring-like potential energy - the total energy in fact of the Universe.

From that potential energy, present in what we now call space, or space-time, which is anything but empty, is spawned all sub-atomic particles - both matter and antimatter. When those particles collide, they mutually annihilate to create photons.

The reverse can also happen under extreme conditions - two photons can collide to create matter and anti-matter. It is potential energy in the spring-coiled Universe that is our "Dark Energy. It may or may not have mass depending on conditions.

A moment when it has no mass is the instant of the Big Bang. Let me briefly explain. An oscillating universe switches between Big Bang and Big Crunch. With the latter gravitation pulls everything into a super blackhole which then becomes a singularity - a massively dense point in space-time.

What prevents it becoming infinitely small - a physical impossibility? Answer: friction. As the sub-atomic plasma contracts and grinds, heat is generated which cannot escape - being a black hole. The temperature rises, ie particles in the plasma move faster and faster. When they reach their maximum velocity - the speed of light- all particles are suddenly transformed into photons, which as we know have no true mass(at least, no rest mass: any mass they have is purely relativistic due to their speed).

Once the entire Universe is a super-concentration of photons, all the gravitational forces in the singularity collapse to zero, or nearly so, and the entire thing blows apart - a new Big Bang, to create yet another cycle (inflation, Big Crunch, implosion etc). The Big Bang creates not just sub-atomic particles - from photon-photon collisions, but space-time itself. To reiterate: that space-time is always suffused with the stored potential energy of our curled-up dimensions (Dark Energy)."